I've been playing around a bit with clusterProfiler to work with RNAseq data. When running my own data I noticed that when I ran the same function repeatedly, I would get different results. This happens for both gseKEGG and gseGO, even when I directly copy the commands I used a minute before, different gene sets are claimed to be enriched. I tried the same with the sample data set that they use in examples for this package and saw the same effect and also tried increasing the number of permutations, which didn't really seem to help. I think I'm missing something obvious - could someone help me out?

Below is the code I was using and the output, as well as the output of sessionInfo if that helps any:

However, it does not explain why two runs of the exact same calculation will return different results even if they are 'similar'. Could you give me some insight into how this is possible and how to circumvent this issue?